MemoteReportApp

Independent Section

Contains tests that are independent of the class of modeled organism, a model's complexity or types of identifiers that are used to describe its components. Parameterization or initialization of the network is not required. See readme for more details.

Consistency

Stoichiometric Consistency

100.0%

Mass Balance

99.1%

This will exclude biomass, exchange and demand reactions as they are unbalanced by definition. It will also fail all reactions where at least one metabolite does not have a formula defined. In steady state, for each metabolite the sum of influx equals the sum of efflux. Hence the net masses of both sides of any model reaction have to be equal. Reactions where at least one metabolite does not have a formula are not considered to be balanced, even though the remaining metabolites participating in the reaction might be. Implementation: For each reaction that isn't a boundary or biomass reaction check if each metabolite has a non-zero elements attribute and if so calculate if the overall element balance of reactants and products is equal to zero.

A total of 10 (0.92%) reactions are mass unbalanced with at least one of the metabolites not having a formula or the overall mass not equal to 0: ACCOAACT, ACCOATT, CTPPCT, ACYLACP, ACYAC, ...

Charge Balance

100.0%

Metabolite Connectivity

100.0%

Disconnected metabolites are not part of any reaction in the model. They are most likely left-over from the reconstruction process, but may also point to network and knowledge gaps. Implementation: Check for any metabolites of the cobra.Model object with emtpy reaction attribute.

A total of 0 (0.00%) metabolites are not associated with any reaction of the model:

Unbounded Flux In Default Medium

100.0%

Sub Total

100%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{99.08 + (4 \cdot 100) +}{(5 \cdot 100)} = 99.87$ $(99.08 + (4 * 100) + )/((5 * 100)) = 99.87$

Annotation - Metabolites

Presence of Metabolite Annotation

100.0%

Metabolite Annotations Per Database

pubchem.compound

0.6%

kegg.compound

84.9%

seed.compound

50.6%

inchikey

0.0%

inchi

0.0%

chebi

82.0%

hmdb

42.4%

reactome

0.0%

metanetx.chemical

80.9%

bigg.metabolite

52.0%

biocyc

49.8%

Metabolite Annotation Conformity Per Database

pubchem.compound

100.0%

kegg.compound

100.0%

seed.compound

100.0%

inchikey

0.0%

inchi

0.0%

chebi

100.0%

hmdb

100.0%

reactome

0.0%

metanetx.chemical

100.0%

bigg.metabolite

100.0%

biocyc

100.0%

Uniform Metabolite Identifier Namespace

100.0%

Sub Total

78%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{0.56 + 84.94 + 50.56 + 82.02 + 42.36 + 80.90 + 52.02 + 49.78 + (10 \cdot 100) + (6 \cdot 0)}{(24 \cdot 100)} = 78.25$ $(0.56 + 84.94 + 50.56 + 82.02 + 42.36 + 80.90 + 52.02 + 49.78 + (10 * 100) + (6 * 0))/((24 * 100)) = 78.25$

Annotation - Reactions

Presence of Reaction Annotation

100.0%

Reaction Annotations Per Database

rhea

52.6%

kegg.reaction

68.5%

seed.reaction

5.8%

metanetx.reaction

66.9%

bigg.reaction

4.3%

reactome

0.0%

ec-code

69.9%

brenda

0.0%

biocyc

2.3%

Reaction Annotation Conformity Per Database

rhea

100.0%

kegg.reaction

100.0%

seed.reaction

100.0%

metanetx.reaction

100.0%

bigg.reaction

100.0%

reactome

0.0%

ec-code

100.0%

brenda

0.0%

biocyc

100.0%

Uniform Reaction Identifier Namespace

100.0%

Sub Total

77%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{52.55 + 68.45 + 5.78 + 66.92 + 4.34 + 69.90 + 2.30 + (9 \cdot 100) + (4 \cdot 0)}{(20 \cdot 100)} = 76.95$ $(52.55 + 68.45 + 5.78 + 66.92 + 4.34 + 69.90 + 2.30 + (9 * 100) + (4 * 0))/((20 * 100)) = 76.95$

Annotation - Genes

Presence of Gene Annotation

100.0%

Gene Annotations Per Database

refseq

0.0%

uniprot

75.7%

ecogene

0.0%

kegg.genes

76.2%

ncbigi

76.2%

ncbigene

0.0%

ncbiprotein

0.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Gene Annotation Conformity Per Database

refseq

0.0%

uniprot

100.0%

ecogene

0.0%

kegg.genes

23.8%

ncbigi

23.8%

A total of 698 gene annotations (76.20%) do not match the regular expression patterns defined on identifiers.org for the ncbigi database: RTMO00131, RTMO05104, RTMO02719, RTMO02716, RTMO00549, ...

ncbigene

0.0%

ncbiprotein

0.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Sub Total

46%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{75.66 + 76.20 + 76.20 + 23.80 + 23.80 + (2 \cdot 100) + (14 \cdot 0)}{(21 \cdot 100)} = 45.86$ $(75.66 + 76.20 + 76.20 + 23.80 + 23.80 + (2 * 100) + (14 * 0))/((21 * 100)) = 45.86$

Annotation - SBO Terms

Metabolite General SBO Presence

100.0%

Metabolite SBO:0000247 Presence

96.9%

Reaction General SBO Presence

100.0%

Metabolic Reaction SBO:0000176 Presence

99.8%

Transport Reaction SBO:0000185 Presence

98.2%

Exchange Reaction SBO:0000627 Presence

100.0%

Demand Reaction SBO:0000628 Presence

100.0%

Sink Reactions SBO:0000632 Presence

Skipped

Gene General SBO Presence

100.0%

Gene SBO:0000243 Presence

100.0%

Biomass Reactions SBO:0000629 Presence

50.0%

Sub Total

86%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{96.85 + 99.79 + 98.21 + 50.00 + (6 \cdot 100) + (1 \cdot 0)}{(11 \cdot 100)} = 85.90$ $(96.85 + 99.79 + 98.21 + 50.00 + (6 * 100) + (1 * 0))/((11 * 100)) = 85.90$

Total Score

88%

The Total Score is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(3 \cdot 99.87) + (1 \cdot 78.25) + (1 \cdot 76.95) + (1 \cdot 45.86) + (2 \cdot 85.90)}{(3 \cdot 100) + (1 \cdot 100) + (1 \cdot 100) + (1 \cdot 100) + (2 \cdot 100)} = 87.88$ $((3 * 99.87) + (1 * 78.25) + (1 * 76.95) + (1 * 45.86) + (2 * 85.90))/((3 * 100) + (1 * 100) + (1 * 100) + (1 * 100) + (2 * 100)) = 87.88$

Total Score

88%

Score per Category

Specific Section

Covers general statistics and specific aspects of a metabolic network that are not universally applicable. See readme for more details.

SBML

SBML Level and Version

Errored

FBC enabled

Errored

Basic Information

Model Identifier

GTModelBeata2015

Total Metabolites

890

Total Reactions

1,176

Total Genes

916

Total Compartments

Metabolic Coverage

1.28

Metabolite Information

Unique Metabolites

810

Duplicate Metabolites in Identical Compartments

Metabolites without Charge

Metabolites without Formula

Medium Components

Reaction Information

Purely Metabolic Reactions

975

Purely Metabolic Reactions with Constraints

Transport Reactions

112

Transport Reactions with Constraints

Thermodynamic Reversibility of Purely Metabolic Reactions

0.34

Reactions With Partially Identical Annotations

0.01

Duplicate Reactions

0.00

Reactions With Identical Genes

0.48

Gene-Protein-Reaction (GPR) Associations

Reactions without GPR

Fraction of Transport Reactions without GPR

0.00

Enzyme Complexes

Biomass

Biomass Reactions Identified

Biomass Consistency

BIOMASSt

0.00

biomass

0.55

Biomass Production In Default Medium

BIOMASSt

0.80

biomass

0.80

Unrealistic Growth Rate In Default Medium

BIOMASSt

false

biomass

false

Biomass Production In Complete Medium

BIOMASSt

44.05

biomass

44.05

Blocked Biomass Precursors In Default Medium

BIOMASSt

biomass

Blocked Biomass Precursors In Complete Medium

BIOMASSt

biomass

Ratio of Direct Metabolites in Biomass Reaction

BIOMASSt

0.00

biomass

0.04

Number of Missing Essential Biomass Precursors

BIOMASSt

biomass

Energy Metabolism

Non-Growth Associated Maintenance Reaction

Growth-associated Maintenance in Biomass Reaction

BIOMASSt

false

biomass

true

Number of Reversible Oxygen-Containing Reactions

Erroneous Energy-generating Cycles

MNXM3

Skipped

MNXM63

Skipped

MNXM51

Skipped

MNXM121

Skipped

MNXM423

Skipped

MNXM6

Skipped

MNXM10

Skipped

MNXM38

Skipped

MNXM208

Skipped

MNXM191

Skipped

MNXM223

Skipped

MNXM7517

Skipped

MNXM12233

Skipped

MNXM558

Skipped

MNXM21

Skipped

MNXM89557

Skipped

Network Topology

Universally Blocked Reactions

148

Orphan Metabolites

Dead-end Metabolites

Stoichiometrically Balanced Cycles

216

Metabolite Production In Complete Medium

219

Metabolite Consumption In Complete Medium

231

Matrix Conditioning

Ratio Min/Max Non-Zero Coefficients

0.00

Independent Conservation Relations

Rank

871

Degrees Of Freedom

305

Experimental Data Comparison

Growth Prediction

Skipped

Gene Essentiality Prediction

Skipped

Misc. Tests

Environment

Python Version 3.6.10

Platform Linux

Memote Version 0.10.2

Package Versions